Australian Jacob Birtwhistle, who had to jump a barrier after wrongly running down the finishing straight as he led on the penultimate lap, was second.
Mola won in 54mins 52 seconds, with South African Richard Murray third.
Olympic silver and bronze medallist Brownlee, 27, finished 23 seconds behind Mola and fellow Briton Grant Sheldon was 10th.
Bermuda’s Flora Duffy, 29, claimed her fourth straight win to dislodge Katie Zaferes at the top of the women’s standings.
“I feel fantastic. I did the best I could, I won another sprint distance, so I think I am performing better, doing better on the swim and doing a better performance overall”, said Mola, who has won two sprint races in a row. “I saw Jake moving on the second lap and I thought it was the end of the world, but I could get back to win”, he said.